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Table 2 Details of the bi-allelic RAD loci and filtered putative SNPs and PSVs in Family 1 and Family 2

From: Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon

  Family 1 Family 2 Commona Total
Total bi-allelic RAD loci 10,238 10,930 6,668 14,500
Bi-allelic RAD loci removed during filteringb 2,109 3,804 797 5,116
Remaining bi-allelic RAD loci 8,130 7,127 5,871 9,386
Bi-allelic RAD loci with both alleles fixed 3,768 3,491 2,674 4,585
Segregating bi-allelic RAD loci 4,362 3,636 3,197 4,801
Putative SNPs 4,725 3,927 1,940 6,712
  1. a Common refers to loci where at least one of the RAD alleles at a RAD marker in family 1 matches exactly to one of the RAD alleles at a RAD marker in family 2. In the case of putative SNPs, common refers to the same SNP segregating in both families at the same position in the RAD marker sequence.
  2. b Filtering criteria given in the ‘Methods’.